2PEB | pdb_00002peb

Crystal structure of a putative dioxygenase (npun_f1925) from nostoc punctiforme pcc 73102 at 1.46 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 
    0.213 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Crystal structure of putative dioxygenase (ZP_00109509.1) from Nostoc punctiforme PCC 73102 at 1.46 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
putative dioxygenase
A, B
122Nostoc punctiforme PCC 73102Mutation(s): 0 
Gene Names: ZP_00109509.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4
Download Ideal Coordinates CCD File 
E [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL
Query on UNL
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]		Unknown ligand
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free:  0.213 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.562α = 90
b = 57.042β = 104.81
c = 46.676γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
SHELXphasing
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
SHARPphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.5: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary